MAGMA: Multiobjective Analyzer for Genetic Marker Acquisition


A genetic mapping project, typically implemented during a search for genes responsible for a disease, requires the acquisition of a set of data from each of a large number of individuals. This data set includes the values of multiple genetic markers. These genetic markers occur at discrete positions along the genome, which is a collection of one or more linear chromosomes. Typing the value of a marker in an individual carries a cost; one seeks to minimize the number of markers typed without excessively jeopardizing the probability of detecting an association between a marker and a disease phenotype.

MAGMA employs a multiobjective evolutionary algorithm to pick tag SNPs
from a larger set of SNPs while balancing multiple objectives (e.g.,
cost and sensitivity). It is based on the ECJ evolutionary software
package written by Sean Luke and includes the Strength Pareto
Evolutionary Algorithm Version 2 changes for multiobjective analysis.
The code runs on any platform with Java Version 2.